Course Outline

Biol 308: Principles of Molecular Biology

Course description

Principles of Molecular Biology (course description from the undergraduate calendar) Prokaryote and eukaryote genome structure and replication; mechanisms of gene expression and regulation. BIOL 308 is recommended for those wishing a general understanding in molecular biology. Students intending to take several upper year molecular biology courses are advised to take BIOL 309 and 308 concurrently. Required as a prerequisite for the following courses: BIOL 331, 403, 428, 431, 434, 438, 441, 442, 448, 484. [Offered: F, S] Prereq: BIOL 130, 239 (previously 139);

The course is delivered ON-LINE using video lectures (using PowerPoint slides), which are posted on the UW-Learn web site (http://learn.uwaterloo.ca). The same lecture powerpoints files (without audio) are also available. Access to the lectures will be available following completion of the Concepts Pre-Test (see Student Assessment, below). Lectures will be released on Mondays for that week and consist of two “sets” of three videos. Individual videos range from 15 – 30 minutes each , and one set of three videos is approximately 80 minutes in length.

It’s recommended that students watch videos weekly. Trying to “binge” several weeks of lectures is not likely to be a successful strategy given the range and complexity of the systems we will examine. Also, there are a FIVE on-line quizzes that also fit into that timeline. These quizzes are organized to coordinate with the different sections of this course, so again, these are best done in-line with your lecture progression. There will be two midterms one in the middle of the term, and one near the end.

Course learning objectives: By the end of this course you should be able to:

- Identify and explain the structure and function of DNA and RNA

- Illustrate prokaryotic and eukaryotic genome organization (or structure) and replication

- Explain mechanisms of gene expression and illustrate different levels of its regulation

Contact information

Course lecturer: Dr. Bruce R. Wolff, (ESC-357D). Please email me directly at: [email protected] . While I won’t be holding official “office hours”, I will do my best to reply to your emails as quickly as possible. Please keep in mind that I might not respond promptly to emails sent on evenings or weekends. In those situations, I will do my best to respond on the next business day.

Resources

Course textbook – Fundamental Molecular Biology (2nd Ed.) by Lizbeth A. Allison.

The textbook is available to students for free from the Library portal:

https://ebookcentral.proquest.com/lib/Waterloo/detail.action?docID=2064699

The link will take you to the Library "portal" where you can login. Once you've done that, you'll see the Fundamental Molecular Biology "page" and options for accessing the e-book

Other good molecular biology books: Cell and Molecular Biology by Karp 9th ed, 2019 (Biol 130 textbook)

        Genes XII (or XI, X) by Lewin, 2018.

        Molecular Biology of the Gene by Watson, et al. 2014, 7th ed

and the previous text (5th Ed): Molecular Biology of the Cell by Alberts et al. 6th ed, 2017

Course website – This course should appear on your listing of courses in http://learn.uwaterloo.ca/. it includes the course lectures (Powerpoint files and mp4), links to relevant web sites, study questions, on-line quizzes and midterms, and additional information and announcements throughout the term.

Course topics

Introduction – approach to molecular biology

Nucleic acid structure and hybridization

• functions of DNA; Central Dogma of molecular biology

• DNA and RNA structure

• DNA shapes and sizes

• denaturation and renaturation of nucleic acids – Cot analysis.

Eukaryotic chromatin structure

Cell cycle and cell division

• cell cycle (brief intro)

• mitosis, meiosis

DNA replication

• DNA replication machinery (general)

• initiation of replication

• prokaryotic and eukaryotic replication machineries

• DNA repair mechanisms

DNA Recombination and DNA rearrangements

• use of DNA repair mechanisms

How/why do we asses transcription rate and level of gene expression

• Brief information re: why/when we perform Southern, northern, western blotting and microarrays

• How do we look for the transcription start site and why

• Nucleic acid – protein interactions and their importance

Transcription: Prokaryotes

• E. coli polymerase and its promoters

• regulation of the lac, ara and trp operons

• regulation of transcriptional initiation

• prokaryotic DNA binding proteins

Transcription: Eukaryotes

• overview of eukaryotic RNAPs

• RNAP II

• transcriptional activators and repressors

• transcription initiation by RNAP II

• molecular mechanisms of eukaryotic initiation of transcription

• transcriptional initiation by other RNAPs

RNA processing and post-transcriptional control of gene expression

• termination of prokaryotic transcripts and attenuation

• splicing of primary transcripts

• capping and polyadenylation

• post-transcriptional control of gene expression

• transport of mRNA from the nucleus

• tRNA and rRNA processing

Translation

• general overview of translation (include codons and tRNA)

• translation initiation

• chain elongation and termination

• post-translational modification

Mitochondrial and Chloroplast genomes

Student Assessment

Concepts Pre-test*

Not Graded

*In order to "unlock" the course notes for download, you will need to complete the Learn Assignment: Biol 308 Concepts pre-test. You need to score at least 30% on the test, and can retake the test if necessary. Once you've scored above 30%, the course notes will be accessible for the rest of the term. This can be accessed in the Submit tab under Quizzes. There are 60 questions, and you have 45 minutes to complete the test. You can retake the test as many times as necessary to achieve 30%.

PLEASE NOTE - this test is for your benefit. The questions asked should be "core knowledge" to someone with the necessary background to do well in Biol 308 Principles of Molecular Biology, so your score should be a signal to you about how well prepared you are for this course. Those who score below 50% should seriously consider reviewing basic Genetics and Cell Biology concepts to avoid falling behind.

Your mark on the pre-test WILL NOT be a part of your final course grade.

On-line Quizzes: must be completed by August 5, 2021.    50%

Quiz #1: Background and DNA Structure (released: May 19)    10%

Quiz #2: Chromosome structure and Replication (released: June 2)    10%

Quiz #3: DNA Repair and Prokaryotic Transcription (released: June 23)    10%

Quiz #4: Operons, Eukaryote Transcription and TF’s (released: July 7)    10%

Quiz #5: mRNA processing, Translation, Organelle DNA (released: July 21)    10%

On-line Exams:    50%

Midterm 1 (June 17, 9am – June 18, 9am : 1 hr. written questions)    25%

Midterm 2 (July 29, 9am – July 30, 9am : 1 hr. written questions)    25%

Participation in Research Study:    2% (Bonus)

This is a bonus mark that can be earned by either:

a. Participating in a broader research project by completing BOTH

• a start of term survey (~10 mins), and

• an end of term survey (~10 mins)

b. Completing a short (250 word) summary of BIOL*308 core concept at end of term

You can also choose to do neither, as this is entirely a bonus mark.

Quizzes and Midterms can be accessed under the “Submit” tab and selecting “Quizzes” from the drop down menu. Either choice will take you to a listing of the on-line assignments and Midterms available at that time. . Please note that quizzes will be released on a schedule that is coordinated with the release of lectures, and the two midterms. Once a quiz is made available, it will stay “open” until the last day of the term at 11: 30 pm (August 5). It is strongly suggested that you complete the quizzes as we finish the relevant course material.

Study questions covering the entire course are provided on the UW-Learn website for Biol 308. study questions are designed to help you learn the material, and they can be downloaded from the web site. I suggest that you answer them as we go thru the lectures, as they will help you prepare for the exams. They are representative of the types of questions that will be on the midterm and final (both in terms of material covered, and style of questions). Please attempt to answer study questions before “asking” for answers. 

The midterms will consist of a small number (less than 10 questions) of short (4 or 5 mark) or long (8-10 mark) written answers to specific questions on topics covered in the lectures in the term. The second midterm (August 4/5) will NOT be cumulative but will cover the material from lectures after the first midterm. More information for midterms will be posted as the term progresses.

Midterm 1 and Midterm 2: 1 hr. duration once you begin.

Participation in Research Study as noted is entirely voluntary and can result in an extra 2% bonus mark. BIOL 308 is taking part in a broader research project that focuses on assessing student connectedness and student awareness of learning/study skills. The researchers will communicate with students by email and possibly via an announcement in LEARN. You will be able to opt out of the study at any time if you choose. More details about the research study will be sent to students over the course of the term.

Note: Students may earn a "bonus" mark for participating in this research by completing the start and end of term surveys. Students not wishing to participate in the research project (i.e. not complete the surveys), may earn the "bonus" mark by completing an alternative assignment. As it is a bonus mark, a student may also decide to do neither activity

Students requiring accommodation

AccessAbility Services collaborates with all academic departments to arrange appropriate accommodations for students with disabilities without compromising the academic integrity of the curriculum. If you require academic accommodations to lessen the impact of your disability, please register with the AAS at the beginning of each academic term. During these times of on-line delivery, please visit the website for contact information:

https://uwaterloo.ca/accessability-services/

Expectations for Change

Given the current COVID-19 crisis, decisions may need to be taken that will directly affect the material covered, the number and weight of the assignments and midterms required, and the distribution of grades among completed and uncompleted components of the course. The university and lecturers will make every effort to keep to this course outline, but students need to be aware that all of these factors may be subject to change if and when conditions change.

Expectation of Academic Integrity

Academic Integrity: In order to maintain a culture of academic integrity, members of the University of Waterloo community are expected to promote honesty, trust, fairness, respect and responsibility.

Grievance: A student who believes that a decision affecting some aspect of his/her university life has been unfair or unreasonable may have grounds for initiating a grievance. Read Policy #70, Student Petitions and Grievances, Section 4. http://www.adm.uwaterloo.ca/infosec/Policies/policy70.htm

Discipline: A student is expected to know what constitutes academic integrity, to avoid committing academic offenses, and to take responsibility for his/her actions. A student who is unsure whether an action constitutes an offense, or who needs help in learning how to avoid offenses (e.g., plagiarism, cheating) or about “rules” for group work/collaboration should seek guidance from the course professor, academic advisor, or the Undergraduate Associate Dean. For information on categories of offenses and types of penalties, students should refer to Policy #71, Student Discipline, http://www.adm.uwaterloo.ca/infosec/Policies/policy71.htm

Appeals: Concerning a decision made under Policy #70 (Student Petitions and Grievances) (other than petitions) or Policy #71 (Student Discipline) a student may appeal the finding, the penalty, or both. A student who believes he/she has a ground for an appeal should refer to Policy #72 (Student Appeals) http://www.adm.uwaterloo.ca/infosec/Policies/policy72.htm

The Faculty of Arts has an excellent website on “Avoiding Academic Offences”, Most of it is very applicable to Science students as well, regardless of the courses they are in. (http://arts.uwaterloo.ca/arts/ugrad/academic_responsibility.html).